Meat Science

2026-10-01

2026 • Volume 240 • Article 110157

10.1016/j.meatsci.2026.110157

Abstract

Ordinal scales are commonly used in subjective meat color evaluations. Although these data appear numeric, they represent ordered categories and analysis with metric models may lead to type I and II errors. This study used a set of trained panel beef subjective color data to demonstrate the application of ordinal models under the Bayesian framework and to compare them with the metric frequentist methodology. Rather than using null hypothesis significance testing and P values from ANOVA, the Bayesian framework allows direct evaluations of pairwise hypothesis through posterior probabilities. Results indicate that averaging observations across panelists resulted in information loss regardless of the statistical approach, thus suggesting evaluators should be modeled as a random effect. The metric ANOVA showed a retail day by location interaction for color uniformity (P = 0.008) and post hoc tests detected no location differences until day 3. Pairwise hypothesis testing using the Bayesian ordinal models was subsequently conducted to directly evaluate the location effect on day 3, and the results supported a location difference consistent with the metric post hoc comparison. Despite similar findings between the methodologies for color uniformity, ordinal models remain more appropriate because they respect the ordered categorical structure of ordinal data. The Bayesian framework provided probabilistic inferences from the posterior distribution, offering results that are more intuitive and informative for interpretation and decision-making.

American Journal of Potato Research

2026-04-29

2026 • Volume 103 • Issue 3 • pp 454–467

10.1007/s12230-026-10053-x

Abstract

Globodera pallida, a quarantine potato cyst nematode (PCN), has had a significant economic impact on the Idaho potato industry. Developing resistant commercial varieties has been challenging because the predominant russet potato market class lacks resistance to G. pallida, and no single major resistance gene has been identified. This study characterized the phenotypic resistance to the Idaho G. pallida pathotype Pa2/3 population in a tetraploid russet potato population derived from PCN-resistant ‘Eden’ and PCN-susceptible ‘Western Russet’. A total of 227 offspring were distributed over three years with a different subset of the population evaluated each year alongside four cultivar controls, and four PCN differential clones. Phenotypic evaluations were conducted under greenhouse conditions to evaluate traits related to cyst and egg development. Progeny showing resistance similar to ‘Eden’ constituted 13.7%, 23.4%, and 18.1% based on cysts, eggs/cyst and eggs/clone, respectively. Identifying resistant progeny through this phenotypic evaluation highlights individuals likely carrying favorable alleles, providing a valuable genetic contribution for breeding programs and research.

The R Journal

2025-10-04

2025 • Volume 17 • Issue 2 • pp 4-14

10.32614/RJ-2025-011

Abstract

CRAN Task Views have been available on the Comprehensive R Archive Network since 2005. They provide guidance about which CRAN packages are relevant for tasks related to a certain topic, and can also facilitate automatic installation of all corresponding packages. Motivated by challenges from the growth of CRAN and the R community as a whole since 2005, all of the task view infrastructure and workflows were rethought and relaunched in 2021/22 in order to facilitate maintenance, and to foster deeper interactions with the R community. The redesign encompassed the establishment of a group of CRAN Task View Editors, moving all task view sources to dedicated GitHub repositories, adopting well-documented workflows with a code of conduct, and leveraging R/Markdown files (rather than XML) for the content of the task views.

Global Change Biology

2025-09-01

2025 • Volume 31 • Issue 3 • pp e70520

10.1111/gcb.70520

Abstract

Global apex scavenger declines strongly alter food web dynamics, but studies rarely test whether trophic downgrading impacts ecosystem functions. Here, we leverage a unique, disease-induced gradient in Tasmanian devil (Sarcophilus harrisii ) population densities to assess feedbacks between carcass persistence, subordinate scavenger guilds, and biogeochemical cycling. We further explored interkingdom and seasonal interactions by manipulating carcass access and replicating experiments in warmer, drier summer versus cooler, wetter winter periods. We show Tasmanian devil declines significantly extend carcass persistence and increase the flux of carcass-derived nutrients belowground (e.g., by 18?134-fold for ammonium). Greater nutrient availability reduces soil microbiome diversity by up to 26%, increasing the relative abundance of putative zoonotic pathogens. Nutrient subsidies also shift microbial communities toward faster-growing taxa that invest less energy in resource acquisition, with implications for soil carbon sequestration. Rates of carcass decomposition were reduced in the winter, dampening soil biogeochemical responses and interkingdom competition. Notably, while less efficient scavenger guilds clearly facilitate carcass consumption, they were not able to fill the functional role of apex scavengers. Our study illustrates how trophic downgrading effects can ripple across all levels of ecological organization.-

Journal of Crop Improvement

2025-05-04

2025 • Volume 39 • Issue 3 • pp 225-250

10.1080/15427528.2025.2489605

Abstract

Genotype-by-environment interaction (GEI) significantly impacts the success of plant breeding strategies in various crops including the cool-season annual crops such as chickpea (Cicer arietinum L.). In this study, advanced trials of 15 spring chickpea genotypes were tested at three locations for multiple years in the Pacific Northwest region of the United States. The normalized difference vegetation index (NDVI), green NDVI (GNDVI), and soil adjusted vegetation index (SAVI) were extracted from unmanned aerial vehicle-based multispectral images at flowering and early pod development. The genotype, environment, and GEI effects on the vegetative indices were evaluated, and compared with those on yield. The G × E models evaluated were the additive main effects and multiplicative interaction (AMMI) and genotype-environment interaction (GGE) biplot. The associated metrics utilized in the study included AMMI stability value (ASV), and genotype stability index (GSI). There were significant genotype and environment effects (p < 0.001) for seed yield and vegetation indices. GEI effects were significant for seed yield, GNDVI at flowering, and SAVI at early pod development. The AMMI, GGE, ASV, and GSI analysis identified two genotypes (G10 and G12) as stable, high-performing genotypes based on seed yield, GNDVI at flowering and SAVI at early pod development data. The findings revealed that the vegetation indices can potentially be valuable, in addition to seed yield, to measure the genotypic performance and the GEI effects of chickpea cultivars. Such evaluation of the GEI effects on crop performance with additional metrics can enhance the variety selection process in the plant breeding programs.

American Journal of Potato Research

2025-04-01

2025 • Volume 102 • Issue 2 • pp 129-151

10.1007/s12230-025-09979-5

Abstract

Management of the Colorado potato beetle (Leptinotarsa decemlineata) is reliant on conventional insecticides that can negatively affect non-target arthropods. Calantha™ (active ingredient: ledprona) is a sprayable double-stranded RNA biopesticide specific for L decemlineata proteasome subunit beta 5 gene that triggers the RNA-interference pathway and is designed to have limited non-target effects. To test this hypothesis, we conducted two years of field trials in Idaho, Wisconsin, and Maine comparing arthropod responses to different insecticide regimes, with and without Calantha, targeting the Colorado potato beetle. Comparisons of arthropod abundance among treatments showed no evidence of effects of Calantha on non-target arthropods, including beneficials (predators, parasitoids), “neutrals” (i.e., non-pests), and other beetle species. Conventional insecticides generally showed more non-target effects, and responses were always stronger for arthropods from vacuum samples than pitfall samples. Insecticide programs featuring Calantha, especially in rotation with other biorational products, may reduce pests while preserving beneficial arthropods and contribute to biological control of arthropod pests in potato fields.

Entomological Generalis

2025-08-19

2025 • Volume 45 • Issue 3 • pp 743-751

10.1127/entomologia/3150

Abstract

The interactions between plant pathogens and their insect vectors may influence vector biology and ecology, which affects pathogen spread. The potato psyllid Bactericera cockerelli (Hemiptera: Triozidae) is the vector of “Candidatus Liberibacter solanacearum” (Lso), the bacterial pathogen associated with zebra chip (ZC) disease in potatoes. Lso is also known to negatively affect potato psyllid’s reproductive output. There are four distinct haplotypes of B. cockerelli identified in the United States, and some of these haplotypes are found overwintering on wild solanaceous hosts. The present study was developed to evaluate the survival of different Lso+ and Lso− potato psyllid haplotypes reared on bittersweet nightshade and cultivated potatoes when exposed to cold temperatures in the laboratory. Lso significantly increased the potato psyllid survivorship in cold temperatures. The potato psyllid survival in the cold tended to be consistently higher when reared on bittersweet nightshade than potato plants. Likewise, the temperatures of 0 ℃ and 4 ℃ were the most favorable for psyllid survival. The observed higher respiration for the Lso+ potato psyllids suggests elevated levels of metabolism at room temperature. Overall, the results presented here indicated that Lso promotes cold tolerance, which should increase the overwintering success of potato psyllids.

American Journal of Potato Research

2025-02-01

2025 • Volume 102 • Issue 1 • pp 51-67

10.1007/s12230-025-09978-6

Abstract

Potato tuber length-to-width ratio (L/W) is an important trait for consumer visual acceptance, pack-out efficiency, French fry production, and waste recovery. In the U.S. Northwest Potato Variety Development Program (NWPVDP), L/W accounts for 13% of the overall postharvest score. Selections with L/W ≥ 1.8 are preferred for maximum raw-product recovery (≥ 7.6-cm-long fries). However, tuber shape often depends on production location. Our objectives were to (1) model the effects of production location on L/W using 26 years of historical data from the NWPVDP, and (2) quantify the variability in tuber shape phenotype of selected NWPVDP varieties across production locations (WA, ID, OR). A mixed linear model demonstrated that tuber L/W was strongly affected by location, year, and location-by-year interactions (40% of total variation), while variety and variety-by-location accounted for 43% of total variation. L/W of the 227-284-g tubers of twenty-two released varieties from the NWPVDP averaged 1.65, 1.70, and 1.92 for WA, OR, and ID, respectively, and ranged from a low of 1.51 and 1.53 (cvs. Payette Russet & Palisade Russet) to a high of 2.06 and 2.12 (cvs. Ranger Russet & Echo Russet) across locations. The round phenotype of Palisade was stable across locations, leading to consistently low fry recovery (84% FW). By contrast, Payette tubers were invariably round in WA and OR, but elongated when grown in ID. The elongated phenotypes of Echo and Ranger from all locations ensured maximum fry recovery (94 to 95% FW), despite the relatively high variation in L/W (9–13%) attributable to location. Collectively, our results suggest an opportunity for genetic selection of L/W that are stable across locations for market specific reductions in shape waste. Future work should focus on identifying key mechanisms which are impacted by production environment for improved stability of L/W. Furthermore, cultural management strategies should be optimized for L/W consistency and usability by all sectors of the potato industry.

Frontiers in Immunology

2024-12-30

2024 • Volume 16 • Article 1532432 • pp 1-13.

https://doi.org/10.3389/fimmu.2024.1532432

Abstract

Mastitis, an inflammatory condition affecting more than 25% of breastfeeding women, is usually associated with reduced milk secretion, pain, and discomfort, which often leads to early cessation of breastfeeding. Although the etiology of mastitis is multifactorial, a pro-inflammatory state of the mammary gland might be a risk factor. However, changes in milk composition, and specifically in the milk immune profile, prior to and during mastitis have not been well described. To help close this research gap, we documented the immune profiles of milk produced by both breasts of 10 women experiencing clinical (CM) and 8 women experiencing subclinical (SCM) mastitis during the week of sign/symptom development as well as the week prior and compared them with milk produced by 14 healthy controls. CM was defined as having signs/symptoms of mastitis, whereas SCM was presumed if the participant did not have signs/symptoms of CM, but her milk had a somatic cell count >400,000 cell/mL and/or sodium-to-potassium (Na/K) ratio >1.0. Concentration of 36 immune factors (including immunoglobulins, cytokines, chemokines, and growth factors) was quantified via immunoassays. Milk produced by women who developed CM had distinct immune profiles the week prior to diagnosis, particularly elevated concentrations of pro-inflammatory cytokine IL-1β and regulatory cytokines IL-2, IL-4 and IL-10. In contrast, immune profiles in milk produced by women with SCM did not differ from that produced by healthy women or those with CM the week prior to mastitis onset. Once mastitis appeared, marked changes in milk’s immune profile were observed in both CM and SCM groups. CM was characterized by elevated concentrations of 27 compounds, including pro-inflammatory cytokines (IL-1β, IL-1ra, and TNFα) and chemokines (including IL-8, eotaxin, IP-10, MCP-1, MIP1α, and MIP1β), compared to healthy controls. Milk’s immune profile during SCM was intermediate, showing higher levels of IL-6, IFNγ, and MCP-1 compared to healthy controls, suggesting a milder, more controlled immune response compared to CM. Only milk produced by the mastitis-affected breast had altered immune profiles. Further research is needed to determine if these differences in milk’s immune profiles can be used to improve mastitis risk prediction prior to onset of symptoms.

Meat and Muscle Biology

2024-08-13

2024 • Volume 8 • Issue 1 • Article 17769 • pp1-14

https://doi.org/10.22175/mmb.17769

Abstract

Chilling-related meat quality issues have been observed in the deep portion of the top round due to the increase of average beef carcass size. The current study examines the impact of an alternative fabrication method aimed at alleviating top round quality in heavy weight beef carcasses (n = 11; 510 kg average weight). Prior to rigor, the knuckle subprimal was partially fabricated to expose the femur on alternating sides of each carcass (TRT), and each adjacent intact side served as a control (CON). All sides were air chilled (2°C) for 48 h before further fabricating. Temperature loggers placed at approximately 2.54 cm below the top round surface was the superficial (SP) location while loggers for the deep (DP) location were inserted at the midline sagittal center of the round until in contact with the femur bone. Temperature and pH decline were monitored for 48 h. The top rounds were collected, aged under vacuum packaging until 14 d postmortem, and then cut into steaks (2.54 cm). Each steak was separated into SP and DP portions and subjected to Warner-Bratzler shear force (WBSF), consumer sensory panel, and a 3-d retail display analysis which included lipid oxidation and objective color evaluation. The TRT accelerated the rate of temperature decline at the DP location (P < 0.001) and increased the pH decline rate at the SP location (P = 0.029). Retail day and location were more impactful than TRT on objective color traits. SP steaks were more tender (P = 0.001) than DP steaks. Consumer taste panel indicated TRT improved overall acceptability (P = 0.042) and flavor (P = 0.035) of top round steaks regardless of locations. TRT accelerated top round DP chilling rate and elevated steak palatability attributes. Findings of the present study report an improvement of top round steaks due to the innovative fabrication treatment.

The Plant Genome

2024-07-31

2024 • Volume 16 • Issue 12 • Article 1876 • pp 1-17

https://doi.org/10.1002/tpg2.20485

Abstract

Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources. Objectives included identifying high-protein pea lines, exploring genetic architecture across environments, pinpointing genes and metabolic pathways associated with high protein, and documenting information for single nucleotide polymorphism (SNP)-based marker-assisted selection. From 2019 to 2021, a 487-accession pea diversity panel, More protein, More pea, More profit, was evaluated in a randomized complete block design. DNA was extracted for genomic analysis via genotype-by-sequencing. Phenotypic analysis included protein and fat measurements in seeds and flower color. Genome-wide association study (GWAS) used multiple models, and the Pathways Association Study Tool was used for metabolic pathway analysis. Significant associations were found between SNPs and pea seed protein and fat concentration. Gene Psat7g216440 on chromosome 7, which targets proteins to cellular destinations, including seed storage proteins, was identified as associated with SPC. Genes Psat4g009200, Psat1g199800, Psat1g199960, and Psat1g033960, all involved in lipid metabolism, were associated with fat concentration. GWAS also identified genes annotated for storage proteins associated with fat concentration, indicating a complex relationship between fat and protein. Metabolic pathway analysis identified 20 pathways related to fat and seven to protein concentration, involving fatty acids, amino acid and protein metabolism, and the tricarboxylic acid cycle. These findings will assist in breeding of high-protein, diverse pea cultivars, and SNPs that can be converted to breeder-friendly molecular marker assays are identified for genes associated with high protein.

Plain Language Summary

Peas are an important crop increasingly valued in the food industry for their protein content. This research aimed to enhance pea seed protein levels by identifying high-protein pea lines and genetic tools. Using a diverse panel of yellow-seeded peas from the USDA ARS gene bank, we conducted a detailed genetic analysis to identify genes and cellular pathways linked to higher protein and fat concentrations in pea seeds. Note that 41 high-protein lines were identified. Genes responsible for protein cellular transportation and those involved in lipid metabolism were found. This knowledge paves the way for breeding peas with high nutritional profiles, meeting agricultural and dietary needs. These findings will help breeders create improved pea cultivars for US farmers and food markets.

Nutrients

2024-06-10

2024 • Volume 16 • Issue 12 • Article 1876 • pp 1-16

https://doi.org/10.3390/nu16121876

Code

Abstract

The objective was to investigate associations of serum vitamin D concentration with depressive symptoms and assess the impact that vitamin D concentration has on the occurrence of depressive symptoms in 20–44-year-old pregnant women, postpartum women, non-pp women (non-pregnant/postpartum women), and men, including a separate subgroup analysis of postpartum breastfeeding and non-breastfeeding women. The study populations were selected from the 2007–2018 NHANES public data. Subjective interview data and objective laboratory data including depressive symptoms, serum vitamin D concentration, nutrient intake, and demographic information were utilized. Two diet patterns were created using principal component analysis, and a Bayesian multinomial model was fit to predict the depression outcomes for each subpopulation. The estimates for the log vitamin D slope parameter were negative for all cohorts; as vitamin D increased, the probability of having no depression increased, while the probability of depression decreased. The pregnant cohort had the steepest vitamin D slope, followed by postpartum women, then non-pp women and men. Higher vitamin D concentration had more impact on decreasing depression risk in pregnant and postpartum women compared to non-pp women and men. Among postpartum women, higher vitamin D concentration had a greater influence on decreasing breastfeeding women’s depression risk than non-breastfeeding women.

Sustainability

2024-01-11

2024 • Volume 16 • Issue 2 • Article 645 • pp 1-23

https://doi.org/10.3390/su16020645

Abstract

This research study underscores the importance of effectively managing soil nutrients in a site-specific manner to enhance crop productivity while considering the spatial variability of the soil. The objective is to identify subfields with similar soil characteristics, referred to as management zones (MZs), to promote sustainable land utilization. This study was conducted in two central pivot fields located in Southern Idaho, USA, where barley and sugar beets were grown. Soil samples were collected from each field in a grid pattern and analyzed for various chemical properties. These properties included soil pH, organic matter, cation exchange capacity, excess lime, electrical conductivity, total inorganic nitrogen, phosphorus, potassium, calcium, magnesium, zinc, iron, manganese, copper, and boron. Descriptive statistics and normality assessments were performed, and the coefficient of variation was calculated to assess the heterogeneity of soil properties, revealing significant variability. To determine the spatial variability of soil properties, ordinary kriging was used revealing diverse spatial patterns for each location and soil variable examined with moderate to strong spatial dependence. To develop the MZs, a combination of principal component analysis and fuzzy k-means clustering was utilized, and specific parameters that represented the overall variability of soil properties in each field were identified. Based on the identified parameters, two clusters were created in each field. The first management zone (MZ1) exhibited lower values of soil pH, excess lime content, and electrical conductivity compared to the MZ2. Consequently, higher crop productivity was observed in MZ1 in both fields. The biomass yields of barley and sugar beets in MZ1 surpassed those in MZ2. This study highlights the effectiveness of the methodology employed to delineate MZs, which can be instrumental in precise soil nutrient management and maximizing crop productivity.

Biological Invasions

2023-03-23

2023 • Volume 25 • pp 2231-2248

https://doi.org/10.1007/s10530-023-03037-z

Abstract

Invasive Hieracium plant species are invading the Greater Yellowstone Ecosystem. The potential distribution of orange hawkweed (Hieracium aurantiacum) and meadow hawkweed (Hieracium caespitosum) were estimated using habitat susceptibility models to assist land managers’ management of these invasive plants. The objectives of this study were to: (1) develop models describing susceptibility of ecosystems to hawkweed invasion, (2) identify indicator species of orange hawkweed and meadow hawkweed, (3) determine habitat types where these invasive hawkweeds might occur, and (4) create habitat susceptibility maps for management planning and ground surveys. Models were developed using a Mahalanobis distance similarity technique from remotely sensed biotic and abiotic variables, as well as known location data for orange and meadow hawkweed. Ground validation was conducted to assess model weaknesses and subsequent model modification. Indicator plant species were identified as surrogates to determine the likelihood of hawkweed presence during ground survey. Transect data collected from areas susceptible to invasion also were used to determine habitat types where hawkweed might occur. The best model included eight variables: north–south aspect, east–west aspect, slope, NDVI, NDWI, blue spectral band, green spectral band, and precipitation. High susceptibility (65+ percent likelihood of suitable habitat) consisted of 66,000 ha for meadow hawkweed and 35,000 ha for orange hawkweed, 5.0% and 2.7% of the study area, respectively. Meadow hawkweed and orange hawkweed had seven and three indicator plant species, respectively. Predicted hawkweed habitat susceptibility encompassed nine habitat types, ranging from xeric sagebrush steppe to wet forests and they overlapped except at the xeric habitat type. Habitat susceptibility models save costs and allow survey prioritization to those areas most susceptible to invasion.

Frontiers in Agronomy

2021-05-23

2021 • Volume 3 • Article 662375 • pp 1-13

https://doi.org/10.3389/fagro.2021.662375

Abstract

Mayweed chamomile (Anthemis cotula L.) is an annual crop weed that has become a substantial impediment to diversify traditional wheat-based cropping systems such as in the Pacific Northwest (PNW), USA. Some of the broadleaf rotational crops are vulnerable to the weed as they are less competitive or lack compatible herbicides for A. cotula management. Although A. cotula has been present in the PNW for more than a century, traits that contribute to invasiveness and how these vary among the weed populations have not been investigated. We assessed trait variation with a common garden greenhouse experiment by comparing 19 A. cotula populations from the PNW and Kashmir Valley, India. Seeds from individual plants from each population were used to grow plants through their senescence. We measured phenological (e.g., flowering duration), morphological (e.g., plant biomass), reproductive fitness (e.g., number of flower heads), and physiological (floral scent VOCs: volatile organic compounds) traits on individual plants and analyzed the data using mixed-effects models. We found high inter-population variation in most of the traits measured, but the variation was not associated with the geographical distance. Seedling emergence within 30 days of planting ranged from 2 to 49% for PNW populations to 55 to 72% for Indian populations. Flowering duration ranged from 2 to 3 months among populations. Other traits such as initial and final flowering dates, the total number of flower heads, and floral scent VOCs also differed among populations. These trait patterns may indicate a localized adaptation of A. cotula populations to environmental or management regimes, variation arising from anthropogenic or natural dispersal, multiple introductions, genetic drift, or combinations of these. Regardless of the processes, the trait variation suggests that weed management plan for A. cotula may need to be tailored to specific locations instead of a uniformly adopted plan across the region.